SKR2 is often loosing contact with Raspbery, and only powering skr down and up helps

Hi!

I have a raspberry 3b+ with SKR2 runing klipper. They are connected via Serial Port. I use Fluidd to control the printer
Often, when I emergency Stop printer from fluidd or just reboot firmware, I get error and raspberry isn’t connecting the skr until I power skr down and up.
I tried to connect via USB, same thing.
Klipper is flashed to skr with 32KiB bootloader and 8MHz Clock reference crystal.

What can be the problem, how can I fix this?